I booked an Orbitz air + hotel package and my itinerary was showing fare details at AA.com which didn't make sense just because the air fare was slightly expensive than the total package price...
Anyway AA posted miles by fare, and I called AAdvantage customer service and told them that's not what I paid.
She told me they needed to investigate and let me know their decision later.
The next day they manually changed fare to distance (special fare).